def __init__(self,
adapter1,
adapter2,
match_probability=RandomMatchProbability(),
insert_max_rmp=1E-6,
adapter_max_rmp=0.001,
min_insert_overlap=1,
max_insert_mismatch_frac=0.2,
min_adapter_overlap=1,
max_adapter_mismatch_frac=0.2,
adapter_check_cutoff=9,
base_probs=dict(p1=0.25, p2=0.75)):
self.adapter1 = adapter1
self.adapter1_len = len(adapter1)
self.adapter2 = adapter2
self.adapter2_len = len(adapter2)
self.match_probability = match_probability
self.insert_max_rmp = insert_max_rmp
self.adapter_max_rmp = adapter_max_rmp
self.min_insert_overlap = min_insert_overlap
self.max_insert_mismatch_frac = float(max_insert_mismatch_frac)
self.min_adapter_overlap = min_adapter_overlap
self.max_adapter_mismatch_frac = float(max_adapter_mismatch_frac)
self.adapter_check_cutoff = adapter_check_cutoff
self.base_probs = base_probs
self.aligner = MultiAligner(max_insert_mismatch_frac,
START_WITHIN_SEQ1 | STOP_WITHIN_SEQ2,
min_insert_overlap)
def test_multi_aligner_no_mismatches():
from atropos._align import MultiAligner
a = MultiAligner(max_error_rate=0, min_overlap=3)
matches = a.locate('AGAGATCAGATGACAGATC', 'GATCA')
assert len(matches) == 2
matches.sort(key=lambda x: x[4], reverse=True)
assert matches[0][0] == 3
assert matches[0][1] == 8
assert matches[0][2] == 0
assert matches[0][3] == 5
assert matches[0][4] == 5
assert matches[0][5] == 0
assert matches[1][0] == 15
assert matches[1][1] == 19
assert matches[1][2] == 0
assert matches[1][3] == 4
assert matches[1][4] == 4
assert matches[1][5] == 0
def test_multi_aligner_with_mismatches():
from atropos._align import MultiAligner
a = MultiAligner(max_error_rate=0.1, min_overlap=10)
matches = a.locate('GATATCAGATGACAGATCAGAGATCAGAT', 'GAGATCAGATGA')
assert len(matches) == 2
matches.sort(key=lambda x: x[5])
assert matches[0][0] == 19
assert matches[0][1] == 29
assert matches[0][2] == 0
assert matches[0][3] == 10
assert matches[0][4] == 10
assert matches[0][5] == 0
assert matches[1][0] == 0
assert matches[1][1] == 12
assert matches[1][2] == 0
assert matches[1][3] == 12
assert matches[1][4] == 11
assert matches[1][5] == 1
